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conversion from poetry to pdm

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sneakers-the-rat 2024-07-01 16:19:13 -07:00
parent d522dd84a5
commit 9eb4f0dec6
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
10 changed files with 3164 additions and 8962 deletions
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4
.gitignore vendored
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@ -162,4 +162,6 @@ cython_debug/
nwb.schema.json
__tmp__
prof
jupyter_execute
jupyter_execute
.pdm-python

22
.readthedocs.yaml
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@ -9,18 +9,24 @@ version: 2
sphinx:
configuration: docs/conf.py
python:
install:
- method: pip
path: docs
build:
os: ubuntu-22.04
tools:
python: "3.11"
jobs:
post_create_environment:
- pip install poetry
- pip install poetry-kernel
- poetry config virtualenvs.create false
post_install:
- poetry install --no-root
#- poetry run python -m ipykernel install --name nwb-linkml_docs
# jobs:
# post_create_environment:
# - pip install poetry
# - pip install poetry-kernel
# - poetry config virtualenvs.create false
# post_install:
# - poetry install --no-root
# #- poetry run python -m ipykernel install --name nwb-linkml_docs
# Optionally build your docs in additional formats such as PDF and ePub
# formats:

39
docs/pyproject.toml Normal file
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@ -0,0 +1,39 @@
[project]
name = "nwb-linkml-docs"
version = "0.1.0"
description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
authors = [
{name = "sneakers-the-rat", email = "JLSaunders987@gmail.com"},
]
license = {text = "AGPL-3.0"}
requires-python = "<3.13,>=3.10"
dependencies = [
# "nwb-linkml",
# "nwb-schema-language",
"sphinx<8.0.0,>=7.2.5",
"furo>=2023.8.19",
"myst-parser>=2.0.0",
"autodoc-pydantic>=2.0.1",
"nptyping>=2.5.0",
"sphinx-autobuild>=2021.3.14",
"nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml",
"nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language",
"sphinx-design>=0.5.0",
"sphinx-togglebutton>=0.3.2",
"myst-nb @ git+https://github.com/executablebooks/MyST-NB.git",
"ipykernel>=6.25.2",
"ipywidgets>=8.1.1",
]
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
check-hidden = true
# ignore-regex = ''
# ignore-words-list = ''

2704
nwb_linkml/poetry.lock generated
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109
nwb_linkml/pyproject.toml
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@ -1,80 +1,57 @@
[tool.poetry]
[project]
name = "nwb-linkml"
version = "0.1.0"
description = "Translating NWB schema language to LinkML"
authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
license = "GPL-3.0"
version = "0.1.0"
authors = [
{name = "sneakers-the-rat", email = "sneakers-the-rat@protonmail.me"},
]
license = {text = "AGPL-3.0"}
readme = "README.md"
requires-python = "<3.13,>=3.10"
dependencies = [
"pyyaml>=6.0",
"linkml-runtime>=1.7.7",
"nwb-schema-language>=0.1.3",
"rich>=13.5.2",
"linkml>=1.7.10",
"nptyping>=2.5.0",
"pydantic>=2.3.0",
"h5py>=3.9.0",
"pydantic-settings>=2.0.3",
"dask>=2023.9.2",
"blosc2>=2.2.7",
"tqdm>=4.66.1",
]
[project.urls]
homepage = "https://nwb-linkml.readthedocs.io"
repository = "https://github.com/p2p-ld/nwb-linkml/"
documentation = "https://nwb-linkml.readthedocs.io"
packages = [
{include = "nwb_linkml", from="src"},
#{include = "nwb_schema_language", from="../nwb_schema_language/src"}
[project.optional-dependencies]
plot = [
"dash<3.0.0,>=2.12.1",
"dash-cytoscape<1.0.0,>=0.3.0",
]
include = [
'src/nwb_linkml/schema/**/*'
]
[tool.poetry.dependencies]
python = ">=3.11,<3.13"
pyyaml = "^6.0"
linkml-runtime = "^1.6.0"
nwb_schema_language = "^0.1.3"
rich = "^13.5.2"
linkml = "^1.6.1"
nptyping = "^2.5.0"
pydantic = "^2.3.0"
h5py = "^3.9.0"
pydantic-settings = "^2.0.3"
dask = "^2023.9.2"
blosc2 = "^2.2.7"
tqdm = "^4.66.1"
dash = {version="^2.12.1", optional=true}
dash-cytoscape = {version="^0.3.0", optional=true}
pytest = { version="^7.4.0", optional=true}
pytest-depends = {version="^1.0.1", optional=true}
coverage = {version = "^6.1.1", optional = true}
pytest-md = {version = "^0.2.0", optional = true}
pytest-cov = {version = "^4.1.0", optional = true}
coveralls = {version = "^3.3.1", optional = true}
pytest-profiling = {version = "^1.7.0", optional = true}
sybil = {version = "^5.0.3", optional = true}
[tool.poetry.extras]
tests = [
"pytest", "pytest-depends", "coverage", "pytest-md",
"pytest-cov", "coveralls", "pytest-profiling", "sybil"
"pytest<8.0.0,>=7.4.0",
"pytest-depends<2.0.0,>=1.0.1",
"coverage<7.0.0,>=6.1.1",
"pytest-md<1.0.0,>=0.2.0",
"pytest-cov<5.0.0,>=4.1.0",
"coveralls<4.0.0,>=3.3.1",
"pytest-profiling<2.0.0,>=1.7.0",
"sybil<6.0.0,>=5.0.3",
]
plot = ["dash", "dash-cytoscape"]
[tool.pdm]
distribution = true
[tool.poetry.group.tests]
optional = true
[tool.poetry.group.tests.dependencies]
pytest = "^7.4.0"
pytest-depends = "^1.0.1"
coverage = "^6.1.1"
pytest-md = "^0.2.0"
pytest-cov = "^4.1.0"
coveralls = "^3.3.1"
pytest-profiling = "^1.7.0"
sybil = "^5.0.3"
[tool.poetry.group.plot]
optional = true
[tool.poetry.group.plot.dependencies]
dash = "^2.12.1"
dash-cytoscape = "^0.3.0"
[tool.pdm.build]
includes = ["src/nwb_linkml", "src/nwb_linkml/schema/**/*"]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.pytest.ini_options]
addopts = [
@ -93,4 +70,4 @@ doctest_optionflags = "NORMALIZE_WHITESPACE"
filterwarnings = [
"ignore::DeprecationWarning",
"ignore:parse_obj:pydantic.PydanticDeprecatedSince20"
]
]

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nwb_schema_language/poetry.lock generated
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53
nwb_schema_language/pyproject.toml
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@ -1,36 +1,39 @@
[tool.poetry]
name = "nwb_schema_language"
[project]
name = "nwb-schema-language"
authors = [
{name = "Jonny Saunders", email = "j@nny.fyi"},
]
license = {text = "AGPL-3.0"}
requires-python = "<3.13,>=3.10"
dependencies = [
"linkml-runtime>=1.7.7",
"pydantic>=2.3.0",
]
version = "0.1.3"
description = "Translation of the nwb-schema-language to LinkML"
authors = ["Jonny Saunders <j@nny.fyi>"]
license = "GNU GPL v3.0"
readme = "README.md"
[project.urls]
homepage = "https://nwb-linkml.readthedocs.io"
repository = "https://github.com/p2p-ld/nwb-linkml/"
documentation = "https://nwb-linkml.readthedocs.io"
packages = [
{ include = "nwb_schema_language", from="src"}
[project.scripts]
run_patches = "nwb_schema_language.patches:main"
[tool.pdm]
[tool.pdm.dev-dependencies]
dev = [
"linkml<2.0.0,>=1.3.5",
"mkdocs-material<9.0.0,>=8.2.8",
"mkdocs-mermaid2-plugin<1.0.0,>=0.6.0",
"schemasheets<1.0.0,>=0.1.14",
]
include = ["README.md", "src/nwb_schema_language/schema", "project"]
[tool.poetry.dependencies]
python = "^3.9"
linkml-runtime = "^1.1.24"
pydantic = "^2.3.0"
[tool.poetry.dev-dependencies]
linkml = "^1.3.5"
mkdocs-material = "^8.2.8"
mkdocs-mermaid2-plugin = "^0.6.0"
schemasheets = "^0.1.14"
[tool.poetry.scripts]
run_patches = 'nwb_schema_language.patches:main'
[tool.pdm.build]
includes = ["src/nwb_schema_language", "README.md", "src/nwb_schema_language/schema", "project"]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.poetry.extras]
docs = ["linkml", "mkdocs-material"]

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poetry.lock generated
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48
pyproject.toml
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@ -1,39 +1,11 @@
[tool.poetry]
name = "nwb-linkml-docs"
version = "0.1.0"
description = "Dependency management to build nwb-linkml docs, see individual packages for actual package deps"
authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
license = "AGPL-3.0"
readme = "README.md"
packages = [
{include = "nwb_linkml", from="nwb_linkml/src"},
{include = "nwb_schema_language", from="nwb_schema_language/src"}
]
[project]
description = "Monorepo root for nwb-linkml"
dependencies = []
requires-python = "<3.13,>=3.10"
[tool.poetry.dependencies]
python = ">=3.11,<3.13"
sphinx = "^7.2.5"
furo = "^2023.8.19"
myst-parser = "^2.0.0"
autodoc-pydantic = "^2.0.1"
nptyping = "^2.5.0"
sphinx-autobuild = "^2021.3.14"
nwb-linkml = { path = './nwb_linkml', develop = true }
nwb_schema_language = { path = './nwb_schema_language', develop = true }
sphinx-design = "^0.5.0"
sphinx-togglebutton = "^0.3.2"
myst-nb = { git = "https://github.com/executablebooks/MyST-NB.git" }
ipykernel = "^6.25.2"
ipywidgets = "^8.1.1"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.lock,*.css,./nwb_linkml/src/nwb_linkml/models,./nwb_linkml/src/nwb_linkml/schema'
check-hidden = true
# ignore-regex = ''
# ignore-words-list = ''
[tool.pdm.dev-dependencies]
dev = [
'-e nwb-linkml @ file:///${PROJECT_ROOT}/nwb_linkml',
'-e nwb-schema-language @ file:///${PROJECT_ROOT}/nwb_schema_language',
'-e docs @ file:///${PROJECT_ROOT}/docs',
]